|
| Status |
Public on Sep 17, 2016 |
| Title |
Go_1 |
| Sample type |
SRA |
| |
|
| Source name |
Hela cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Go 6983
dose: 10 uM
time: 6 hours
biological replicate: 1
experiment number: Exp 5
|
| Treatment protocol |
Drugs were added to cells and DMSO was added at the same amount for the control.
|
| Growth protocol |
Hela cells were cultured in DMEM and plated in 10cm plates the day prior to drug treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed and harvested using Qiagen RNeasy mini kit. 10ug of RNA was DNAse treated and cleaned up with Rneasy MinElute Cleanup Kit.
Total stranded RNA libraries were construced with a standard dUTP protocol. For a the drug screen the previously published Tag-Seq protocol was followed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
fastq trimming with fastx v0.0.13
alignment with STAR v2.2.1
mapped to RefSeq with bedtools v2.25.0
TSS and PAS centered count files generated with metaseq v0.5.6
genes of length greather than 10kb or 250kb were filted with different bed files.
genome build: hg19
Supplementary_files_format_and_content: Read counts by gene (rows) and TSS or PAS distance (columns). Each row is a gene, and each column is a 200 bp bin at a position relative to the TSS or PAS, with the first half of columns upstream and the 2nd half downstream of the TSS/PAS. (This is upstream and downstream are in genomic coordinates, not corrected for gene orientation.) For TSS_500arrays, each column is a 50bp bin around the TSS. In the filenames, F denotes reads aligning to the negative genomic strand, R denotes reads aligning to the positive genomic strand, Pos includes only annotated genes on the positive genomic strand, and Neg includes only annotated genes on the negative genomic strand.
|
| |
|
| Submission date |
Sep 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
jesse M gray |
| E-mail(s) |
jesse.gray@gmail.com
|
| Phone |
6174321877
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Lab |
Gray lab
|
| Street address |
77 avenue louis pasteur, NRB 356
|
| City |
boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE86857 |
A total RNA-Seq screen reveals that the splicing inhibitor Isoginkgetin blocks transcription elongation |
|
| Relations |
| BioSample |
SAMN05784467 |
| SRA |
SRX2254603 |
